Ecosyste.ms: Papers

10.1016/j.xpro.2021.100417

Identifying cytokine signaling signatures in primary human Th-1 cells by phospho-proteomics analysis
Cited by: 0
Author(s): Jonathan Martínez-Fábregas, Elizabeth Pöhler, Ignacio Moraga
Software Mentions: 2
Published: over 3 years ago

10.3390/proteomes6040039

Exploring Morphine-Triggered PKC-Targets and Their Interaction with Signaling Pathways Leading to Pain via TrkA
Cited by: 12
Author(s): Darlene Aparecida Pena, Mariana Lemos Duarte, Dimitrius T. Pramio, Lakshmi A. Devi, Deborah Schechtman
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.ppat.1009351

A unique GCN5 histone acetyltransferase complex controls erythrocyte invasion and virulence in the malaria parasite Plasmodium falciparum
Cited by: 19
Author(s): Jun Miao, Chengqi Wang, Amuza Byaruhanga Lucky, Xiaoying Liang, Hui Min, Swamy Rakesh Adapa, Rays H. Y. Jiang, Kami Kim, Liwang Cui
Software Mentions: 2
Published: over 3 years ago

10.3390/proteomes7010010

Comparative Proteomic Analysis Unveils Critical Pathways Underlying the Role of Nitrogen Fertilizer Treatment in American Elderberry
Cited by: 1
Author(s): Bo Yang, Andrew L. Thomas, C. Michael Greenlief
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pbio.3000774

Cell–substrate adhesion drives Scar/WAVE activation and phosphorylation by a Ste20-family kinase, which controls pseudopod lifetime
Cited by: 24
Author(s): Shashi P. Singh, Peter A. Thomason, Sérgio Lilla, Matthias Schaks, Qian Tang, Bruce L. Goode, Laura M. Machesky, Klemens Rottner, Robert H. Insall
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.ppat.1008917

Novel Babesia bovis exported proteins that modify properties of infected red blood cells
Cited by: 15
Author(s): Hassan Hakimi, Thomas J. Templeton, Minoru Sakaguchi, Junya Yamagishi, Shuichi Miyazaki, Kazuhide Yahata, Takayuki Uchihashi, Shin-ichiro Kawazu, O. Kaneko, Masahito Asada
Software Mentions: 2
Published: about 4 years ago

10.1002/btpr.2978

Multiplexed clonality verification of cell lines for protein biologic production
Cited by: 4
Author(s): Sofie A. O’Brien, Juhi Ojha, Paul Y K Wu, Wei Shou Hu
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-019-5817-8

Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi
Cited by: 16
Author(s): Mari Mäkinen, Jaana Kuuskeri, Pia Laine, Olli‐Pekka Smolander, Andriy Kovalchuk, Zhen Zeng, Fred O. Asiegbu, Lars Paulín, Petri Auvinen, Taina Lundell
Software Mentions: 2
Published: over 5 years ago

10.1126/sciadv.aba8397

The structures of natively assembled clathrin-coated vesicles
Cited by: 38
Author(s): Mohammadreza Paraan, Joshua H. Mendez, Savanna R. Sharum, Danielle L. Kurtin, Huan He, Scott M. Stagg
Software Mentions: 2
Published: over 4 years ago

10.1126/sciadv.abg4102

A microbial eukaryote with a unique combination of purple bacteria and green algae as endosymbionts
Cited by: 19
Author(s): Sergio A. Muñoz-Gómez, M. Kreutz, Sebastian Hess
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-15-S12-S2

Time-course human urine proteomics in space-flight simulation experiments
Cited by: 22
Author(s): Hans Binder, Henry Wirth, Arsen Arakelyan, Kathrin Lembcke, Evgeny S. Tiys, В. А. Иванисенко, Н. А. Колчанов, Alexey Kononikhin, Igor Popov, E. N. Nikolaev, Л. Х. Пастушкова, И. М. Ларина
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep15443

Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations
Cited by: 75
Author(s): Abdallah Abdallah, Grant A. Hill-Cawthorne, Thomas D. Otto, Francesc Español i Coll, José Afonso Guerra-Assunção, Ge Gao, Raeece Naeem, Hifzur Rahman Ansari, Tareq B. Malas, Sabir A. Adroub, Theo Verboom, Roy Ummels, Huoming Zhang, Aswini K. Panigrahi, Ruth McNerney, Roland Brosch, Taane G. Clark, Marcel A. Behr, Wilbert Bitter, Arnab Pain
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.ppat.1009506

The antiviral sirtuin 3 bridges protein acetylation to mitochondrial integrity and metabolism during human cytomegalovirus infection
Cited by: 16
Author(s): Xuanyu Sheng, Ileana M. Cristea
Software Mentions: 2
Published: over 3 years ago

10.3390/proteomes7020014

Extracellular Vesicle Integrins Distinguish Unique Cancers
Cited by: 43
Author(s): Stephanie N. Hurwitz, David G. Meckes
Software Mentions: 2
Published: over 5 years ago

10.3934/Neuroscience.2019.4.299

Brain proteomics links oxidative stress with metabolic and cellular stress response proteins in behavioural alteration of Alzheimer’s disease model rats
Cited by: 3
Author(s): Mohammad Azizur Rahman, Shahdat Hossain, Noorlidah Abdullah, Norhaniza Aminudin
Software Mentions: 2
Published: almost 6 years ago

10.1038/srep37643

Nucleoside-Diphosphate-Kinase of P. gingivalis is Secreted from Epithelial Cells In the Absence of a Leader Sequence Through a Pannexin-1 Interactome
Cited by: 25
Author(s): Kalina R. Atanasova, Jungnam Lee, JoAnn S. Roberts, Kyulim Lee, David M. Ojcius, Özlem Yılmaz
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.ppat.1006001

The Listeria monocytogenes PASTA Kinase PrkA and Its Substrate YvcK Are Required for Cell Wall Homeostasis, Metabolism, and Virulence
Cited by: 61
Author(s): Daniel A. Pensinger, Kyle Boldon, Grischa Y. Chen, William J.B. Vincent, Sherman Kyle, Min Xiong, Adam J. Schaenzer, Emily R. Forster, Jörn Coers, Rob Striker, John-Demian Sauer
Software Mentions: 2
Published: about 8 years ago

10.1038/srep43959

Locus-specific Retention Predictor (LsRP): A Peptide Retention Time Predictor Developed for Precision Proteomics
Cited by: 12
Author(s): Wenyuan Lu, Xiaohui Liu, Shanshan Liu, Weiqian Cao, Yang Zhang, Pengyuan Yang
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-018-4890-8

A high-density genetic map of extra-long staple cotton (Gossypium barbadense) constructed using genotyping-by-sequencing based single nucleotide polymorphic markers and identification of fiber traits-related QTL in a recombinant inbred line population
Cited by: 24
Author(s): Fan Lü, Liping Wang, Xinyi Wang, Haiyan Zhang, Yanfei Zhu, Jiayan Guo, Wenwei Gao, Hao Geng, Quanjia Chen, Yanying Qu
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-015-2262-1

Transcriptome and proteome dynamics in larvae of the barnacle Balanus Amphitrite from the Red Sea
Cited by: 13
Author(s): Kondethimmanahalli H. Chandramouli, Sarah Al-Aqeel, Taewoo Ryu, Huoming Zhang, Loqmane Seridi, Yanal Ghosheh, Pei‐Yuan Qian, Timothy Ravasi
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2164-15-945

Development and bin mapping of gene-associated interspecific SNPs for cotton (Gossypium hirsutum L.) introgression breeding efforts
Cited by: 25
Author(s): Amanda M. Hulse‐Kemp, Hamid Ashrafi, Xiuting Zheng, Fei Wang, Kevin A. Hoegenauer, Andrea Maeda, Shanshan Yang, Kevin Stoffel, Marta Matvienko, Kimberly Clemons, Joshua A. Udall, Allen Van Deynze, Don C. Jones, David M. Stelly
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.ppat.1008086

Nedd8 hydrolysis by UCH proteases in Plasmodium parasites
Cited by: 16
Author(s): Maryia Karpiyevich, Sophie H. Adjalley, Marco Mol, David B. Ascher, Bethany Mason, Gerbrand J. van der Heden van Noort, Heike Laman, Huib Ovaa, Marcus Lee, Katerina Artavanis‐Tsakonas
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.ppat.1005640

Small RNA-Based Antiviral Defense in the Phytopathogenic Fungus Colletotrichum higginsianum
Cited by: 71
Author(s): Sonia Campo, Kerrigan B. Gilbert, James C. Carrington
Software Mentions: 2
Published: over 8 years ago

10.1186/s13068-018-1350-2

Effects of amino acids on the lignocellulose degradation by Aspergillus fumigatus Z5: insights into performance, transcriptional, and proteomic profiles
Cited by: 19
Author(s): Jiaxi Miao, Mengmeng Wang, Lei Ma, Tuo Li, Qiwei Huang, Dongyang Liu, Qirong Shen
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.ppat.1003830

Lysine Acetyltransferase GCN5b Interacts with AP2 Factors and Is Required for Toxoplasma gondii Proliferation
Cited by: 61
Author(s): Jiachen Wang, Stacy E. Dixon, Li Min Ting, Ting-Kai Liu, Victoria Jeffers, Matthew McKnight Croken, Myrasol Calloway, Dominique Cannella, Mohamed‐Ali Hakimi, Kami Kim, William J. Sullivan
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.ppat.1008307

An activator of G protein-coupled receptor and MEK1/2-ERK1/2 signaling inhibits HIV-1 replication by altering viral RNA processing
Cited by: 7
Author(s): Raymond Wong, Ahalya Balachandran, Peter K. Cheung, Ran Cheng, Qun Pan, Peter Stoilov, P. Richard Harrigan, Benjamin J. Blencowe, Donald R. Branch, Alan Cochrane
Software Mentions: 2
Published: almost 5 years ago

10.3390/proteomes8030014

A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field
Cited by: 133
Author(s): Emmalyn J. Dupree, Madhuri Jayathirtha, Hannah Yorkey, Marius Mihăşan, Brîndușa Alina Petre, Costel C. Darie
Software Mentions: 2
Published: over 4 years ago

10.1038/srep33935

A novel affinity-based method for the isolation of highly purified extracellular vesicles
Cited by: 318
Author(s): Wataru Nakai, Takeshi Yoshida, Diego Díez, Yuji Miyatake, Takahiro Nishibu, Naoko Imawaka, Ken Naruse, Yoshifusa Sadamura, Rikinari Hanayama
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-019-53268-1

Elemental Zn and its Binding Protein Zinc-α2-Glycoprotein are Elevated in HPV-Positive Oropharyngeal Squamous Cell Carcinoma
Cited by: 8
Author(s): Kate Poropatich, Tatjana Paunesku, Alia Zander, Brian Wray, Matthew J. Schipma, Prarthana Dalal, Mark Agulnik, Si Chen, Barry Lai, Olga Antipova, Evan Maxey, Koshonna Brown, Michael Beau Wanzer, Demirkan Gursel, Hanli Fan, Alfred Rademaker, Gayle E. Woloschak, Bharat B. Mittal
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms21020466

Identification of 56 Proteins Involved in Embryo–Maternal Interactions in the Bovine Oviduct
Cited by: 13
Author(s): Charles Banliat, Guillaume Tsikis, Valérie Labas, Ana-Paula Teixeira-Gomes, Emmanuelle Com, Régis Lavigne, Charles Pineau, Benoît Guyonnet, Pascal Mermillod, Marie Saint‐Dizier
Software Mentions: 2
Published: almost 5 years ago

10.1186/s13321-019-0391-2

Dataset’s chemical diversity limits the generalizability of machine learning predictions
Cited by: 59
Author(s): Marta Glavatskikh, Jules Leguy, Gilles Hunault, Thomas Cauchy, Benoit Da Mota
Software Mentions: 2
Published: about 5 years ago

10.1186/1758-2946-5-5

Drug-likeness analysis of traditional Chinese medicines: 2. Characterization of scaffold architectures for drug-like compounds, non-drug-like compounds, and natural compounds from traditional Chinese medicines
Cited by: 23
Author(s): Sheng Tian, Youyong Li, Junmei Wang, Xiaojie Xu, Lei Xu, Xiaohong Wang, Lei Chen, Tingjun Hou
Software Mentions: 2
Published: almost 12 years ago

10.1172/JCI86924

Extracellular matrix proteomics identifies molecular signature of symptomatic carotid plaques
Cited by: 108
Author(s): Sarah R. Langley, Karin Willeit, Athanasios Didangelos, Ljubica Matic, Philipp Skroblin, Javier Barallobre-Barreiro, Mariette Lengquist, Gregor Rungger, Alexander Kapustin, Ludmilla Kedenko, Chris Molenaar, Ruifang Lu, Temo Barwari, Gonca Suna, Xiaoke Yin, Bernhard Iglseder, Bernhard Paulweber, Peter Willeit, Joseph Shalhoub, Gérard Pasterkamp, Alun H. Davies, Claudia Monaco, Ulf Hedin, Catherine M. Shanahan, Johann Willeit, Stefan Kiechl, Manuel Mayr
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-9-595

Genome wide survey, discovery and evolution of repetitive elements in three Entamoeba species
Cited by: 53
Author(s): Hernán Lorenzi, Mathangi Thiagarajan, Brian J. Haas, Jennifer Wortman, Neil Hall, Elisabet Caler
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12864-019-6194-z

The olfactory secretome varies according to season in female sheep and goat
Cited by: 7
Author(s): P A Cann, Malika Chabi, Aliénor Delsart, Chrystelle Le Danvic, Jean‐Michel Saliou, Manon Chasles, Matthieu Keller, Patricia Nagnan‐Le Meillour
Software Mentions: 2
Published: about 5 years ago

10.1016/j.mbplus.2020.100027

Proteomic fingerprints of damage in extracellular matrix assemblies
Cited by: 18
Author(s): Alexander Eckersley, Matiss Ozols, Ronan O’Cualain, Emma-Jayne Keevill, April Foster, Suzanne M. Pilkington, David Knight, Christopher E.M. Griffiths, Rachel Watson, Michael J. Sherratt
Software Mentions: 2
Published: almost 5 years ago

10.14814/phy2.12035

Clathrin complexes with the inhibitor kappa B kinase signalosome: imaging the interactome
Cited by: 5
Author(s): Fabia Gamboni, Guillermo A. Escobar, Ernest E. Moore, Monika Dzieciątkowska, Kirk C. Hansen, Sanchayita Mitra, Trevor A. Nydam, Christopher C. Silliman, Anirban Banerjee
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2407-11-368

Purine Nucleoside Phosphorylase mediated molecular chemotherapy and conventional chemotherapy: A tangible union against chemoresistant cancer
Cited by: 11
Author(s): Preetinder Singh, Swapna Joshi, Pamela J. Russell, Sham V. Nair, Aparajita Khatri
Software Mentions: 2
Published: about 13 years ago

10.1016/j.jbc.2021.100912

Cryo-EM reveals conformational flexibility in apo DNA polymerase ζ
Cited by: 4
Author(s): Chloe D. Truong, Theodore A. Craig, Gaofeng Cui, Maria Victoria Botuyan, Rachel A. Serkasevich, Kayi Y. Chan, Georges Mer, Po-Lin Chiu, Rajiv Kumar
Software Mentions: 2
Published: over 3 years ago

10.1242/jcs.154880

Tyrosine phosphorylation of WIP releases bound WASP and impairs podosome assembly in macrophages
Cited by: 15
Author(s): Vineetha Vijayakumar, James Monypenny, Xing Judy Chen, Laura M. Machesky, Sérgio Lilla, Adrian J. Thrasher, Inés M. Antón, Yolanda Calle, Gareth E. Jones
Software Mentions: 2
Published: almost 11 years ago

10.1074/jbc.RA119.010486

Moonlighting matrix metalloproteinase substrates: Enhancement of proinflammatory functions of extracellular tyrosyl-tRNA synthetase upon cleavage
Cited by: 14
Author(s): Parker G. Jobin, Nestor Solis, Yoan Machado, Peter A. Bell, K. Simran, Nam Hoon Kwon, Sung Hoon Kim, Christopher M. Overall, Georgina S. Butler
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.32866

Mfn2 ubiquitination by PINK1/parkin gates the p97-dependent release of ER from mitochondria to drive mitophagy
Cited by: 243
Author(s): Gian‐Luca McLelland, Thomas Goiran, Wei Yi, Geneviève Dorval, Carol X Chen, Nadine Lauinger, Andrea I Krahn, Sepideh Valimehr, Aleksandar Raković, Isabelle Rouiller, Thomas M. Durcan, Jean‐François Trempe, Edward A. Fon
Software Mentions: 2
Published: over 6 years ago

10.1074/jbc.M116.729806

Composition and Activity of the Non-canonical Gram-positive SecY2 Complex
Cited by: 8
Author(s): Mikaila Bandara, Robin A. Corey, Remy Martin, J. Mark Skehel, Ariel Blocker, Howard F. Jenkinson, Ian Collinson
Software Mentions: 2
Published: about 8 years ago

10.3390/mps3010015

A Fast and Accurate Method to Identify and Quantify Enzymes in Brush-Border Membranes: In Situ Hydrolysis Followed by Nano LC-MS/MS
Cited by: 7
Author(s): Antonio Brun, Melisa E Magallanes, Carlos Martı́nez del Rio, Gregory A. Barrett-Wilt, William H. Karasov, Enrique Caviedes‐Vidal
Software Mentions: 2
Published: almost 5 years ago

10.1074/jbc.RA119.012517

Phosphorylation of the overlooked tyrosine 310 regulates the structure, aggregation, and microtubule- and lipid-binding properties of Tau
Cited by: 27
Author(s): Nadine Ait-Bouziad, Anass Chiki, Galina Limorenko, Shifeng Xiao, David Eliezer, Hilal A. Lashuel
Software Mentions: 2
Published: over 4 years ago

10.1128/IAI.00537-19

Proximity Labeling To Map Host-Pathogen Interactions at the Membrane of a Bacterium-Containing Vacuole in Chlamydia trachomatis-Infected Human Cells
Cited by: 21
Author(s): Macy G. Olson, Ray E. Widner, Lisa M. Jorgenson, Alyssa Lawrence, Dragana Lagundžin, Nicholas T. Woods, Scot P. Ouellette, Elizabeth A. Rucks
Software Mentions: 2
Published: about 5 years ago

10.1007/s00726-021-03006-7

Gamma-gliadin specific celiac disease antibodies recognize p31-43 and p57-68 alpha gliadin peptides in deamidation related manner as a result of cross-reaction
Cited by: 7
Author(s): Ádám Diós, Rita Elek, Ildikò Szabó, Szilvia Horváth, Judit Gyimesi, Róbert Király, Katharina Werkstetter, Sibylle Koletzko, László Fésüs, Ilma Rita Korponay-Szabó
Software Mentions: 2
Published: over 3 years ago

10.1038/hortres.2016.29

Relative quantification of phosphoproteomic changes in grapevine (Vitis vinifera L.) leaves in response to abscisic acid
Cited by: 14
Author(s): Supakan Rattanakan, Iniga S. George, Paul A. Haynes, Grant R. Cramer
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.09073

An ancient Pygo-dependent Wnt enhanceosome integrated by Chip/LDB-SSDP
Cited by: 45
Author(s): Marc Fiedler, Michael Graeb, Juliusz Mieszczanek, Trevor J. Rutherford, Christopher M. Johnson, Mariann Bienz
Software Mentions: 2
Published: about 9 years ago

10.3390/jcm10112446

Characteristics of the Urinary Proteome in Women with Overactive Bladder Syndrome: A Case-Control Study
Cited by: 1
Author(s): Marianne Koch, Pavel Lyatoshinsky, Goran Mitulović, Barbara Bodner‐Adler, Sören Lange, Engelbert Hanzal, Wolfgang Umek
Software Mentions: 2
Published: over 3 years ago

10.1186/s12934-019-1243-5

Redesigning the Aspergillus nidulans xylanase regulatory pathway to enhance cellulase production with xylose as the carbon and inducer source
Cited by: 4
Author(s): P. Ballmann, Jorge D. Lightfoot, Majon Muller, Stefan Dröge, Rolf A. Prade
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.506

Human hair shaft proteomic profiling: individual differences, site specificity and cuticle analysis
Cited by: 48
Author(s): Chelsea Nicole Laatsch, Blythe Durbin‐Johnson, David M. Rocke, Sophie Mukwana, Abby B. Newland, Michael J. Flagler, Michael Davis, Richard A. Eigenheer, Brett S. Phinney, Robert H. Rice
Software Mentions: 2
Published: over 10 years ago

10.1186/s13075-019-1961-4

Proteomic and histopathological characterisation of sicca subjects and primary Sjögren’s syndrome patients reveals promising tear, saliva and extracellular vesicle disease biomarkers
Cited by: 58
Author(s): Lara A. Aqrawi, Hilde Kanli Galtung, Eduarda Guerreiro, Reidun Øvstebø, Bernd Thiede, Tor Paaske Utheim, Xiangjun Chen, Øygunn Aass Utheim, Øyvind Palm, Kathrine Skarstein, Janicke Liaaen Jensen
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.32660

Intracellular antibody signalling is regulated by phosphorylation of the Fc receptor TRIM21
Cited by: 53
Author(s): Claire F. Dickson, Adam J. Fletcher, Marina Vaysburd, Ji‐Chun Yang, Donna L. Mallery, Jingwei Zeng, Christopher M. Johnson, Stephen H. McLaughlin, Mark Skehel, Sarah Maslen, James Cruickshank, Nicolas Huguenin‐Dezot, Jason W. Chin, David Neuhaus, Leo C. James
Software Mentions: 2
Published: over 6 years ago

10.1186/s13059-016-0951-y

OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees
Cited by: 65
Author(s): Song Gao, Denis Bertrand, Burton K. Chia, Niranjan Nagarajan
Software Mentions: 2
Published: over 8 years ago

10.1107/S2059798315022482

Initiating heavy-atom-based phasing by multi-dimensional molecular replacement
Cited by: 3
Author(s): Bjørn Panyella Pedersen, Pontus Gourdon, Xiangyu Liu, Jesper Lykkegaard Karlsen, Poul Nissen
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.7352

Comprehensive map and functional annotation of the mouse white adipose tissue proteome
Cited by: 7
Author(s): Xiaonan Tang, Juan Li, Weigang Zhao, Hui Sun, Jing Li, Zhu-Fang She, Tao Yuan, Shuainan Liu, Quan Liu, Yong Fu, Wei Sun
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-021-07678-z

ddRAD sequencing: an emerging technology added to the biosecurity toolbox for tracing the origin of brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae)
Cited by: 6
Author(s): Yan Ji, Gábor Vétek, Chandan Pal, Jinping Zhang, Rania Gmati, Qing-Hai Fan, Disna N. Gunawardana, Allan Burne, Diane Anderson, K. B. Rebijith, Sherly George, Péter Farkas, Dongmei Li
Software Mentions: 2
Published: over 3 years ago

10.3390/genes10090650

Affinity Purification of NF1 Protein–Protein Interactors Identifies Keratins and Neurofibromin Itself as Binding Partners
Cited by: 11
Author(s): Rachel M. Carnes, Robert A. Kesterson, Bruce R. Korf, James A. Mobley, Deeann Wallis
Software Mentions: 2
Published: about 5 years ago

10.1534/g3.115.017053

The Mosaic Mutants of Cucumber: A Method to Produce Knock-Downs of Mitochondrial Transcripts
Cited by: 9
Author(s): Angel R. Del Valle-Echevarria, Agnieszka Kiełkowska, Grzegorz Bartoszewski, Michael J. Havey
Software Mentions: 2
Published: over 9 years ago

10.1534/genetics.119.302851

Imipridone Anticancer Compounds Ectopically Activate the ClpP Protease and Represent a New Scaffold for Antibiotic Development
Cited by: 30
Author(s): Samuel Jacques, Almer M. van der Sloot, Caroline Huard, Jasmin Coulombe-Huntington, Sarah Tsao, Sylvain Tollis, Thierry Bertomeu, Elizabeth Culp, Daniel Pallant, Michael A. Cook, Éric Bonneil, Pierre Thibault, Gerard D. Wright, Mike Tyers
Software Mentions: 2
Published: over 4 years ago

10.3389/fnsyn.2017.00013

Activity-Dependent Phosphorylation by CaMKIIδ Alters the Ca2+ Affinity of the Multi-C2-Domain Protein Otoferlin
Cited by: 12
Author(s): Sandra Meese, A. Cepeda, Felix Gahlen, Christopher M. Adams, Ralf Ficner, Anthony J. Ricci, Stefan Heller, Ellen Reisinger, Meike Herget
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-015-2076-1

Molt-dependent transcriptomic analysis of cement proteins in the barnacle Amphibalanus amphitrite
Cited by: 31
Author(s): Wenxu Zheng, Dagmar H. Leary, Jinny Liu, Robert E. Settlage, Kenan P. Fears, Stella H. North, Anahita Mostaghim, Tara Essock‐Burns, Sarah E. Haynes, Kathryn J. Wahl, Christopher M. Spillmann
Software Mentions: 2
Published: about 9 years ago

10.3389/fvets.2020.584948

Protein Cargo of Extracellular Vesicles From Bovine Follicular Fluid and Analysis of Their Origin From Different Ovarian Cells
Cited by: 19
Author(s): Svetlana Uzbekova, Carmen Almiñana, Valérie Labas, Ana-Paula Teixeira-Gomes, Lucie Combes‐Soia, Guillaume Tsikis, Anaïs Vitorino Carvalho, Rustem Uzbekov, Г. Н. Сингина
Software Mentions: 2
Published: about 4 years ago

10.1186/gb-2012-13-2-r11

Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells
Cited by: 54
Author(s): Najeeb U. Siddiqui, Xiao Li, Hua Luo, Angelo Karaiskakis, Huayun Hou, Thomas Kislinger, J. Timothy Westwood, Quaid Morris, Howard D. Lipshitz
Software Mentions: 2
Published: almost 13 years ago

10.1038/hortres.2014.39

Dynamic changes in the date palm fruit proteome during development and ripening
Cited by: 35
Author(s): Claudius Marondedze, Chris Gehring, Ludivine Thomas
Software Mentions: 2
Published: over 10 years ago

10.3389/fpls.2017.01292

Stress-Related Mitogen-Activated Protein Kinases Stimulate the Accumulation of Small Molecules and Proteins in Arabidopsis thaliana Root Exudates
Cited by: 13
Author(s): Nadine Strehmel, Wolfgang Hoehenwarter, Susann Mönchgesang, Petra Majovsky, Sylvia Krüger, Dierk Scheel, Justin Lee
Software Mentions: 2
Published: over 7 years ago

10.3389/fbioe.2020.00882

Cell Reprogramming With CRISPR/Cas9 Based Transcriptional Regulation Systems
Cited by: 26
Author(s): K. M. Shakirova, Viktoriia Y. Ovchinnikova, Э. Б. Дашинимаев
Software Mentions: 2
Published: over 4 years ago

10.3389/fpls.2020.01230

Big Genes, Small Effectors: Pea Aphid Cassette Effector Families Composed From Miniature Exons
Cited by: 6
Author(s): Matthew Dommel, Jong‐Nam Oh, José C. Huguet‐Tapia, Endrick Guy, Hélène Boulain, Akiko Sugio, M. Murugan, Fabrice Legeai, Michelle Heck, Charlotte M. Smith, Frank F. White
Software Mentions: 2
Published: about 4 years ago

10.1186/s13072-016-0087-z

Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers
Cited by: 23
Author(s): Jian Sun, Yilin Zhao, Rebecca McGreal, Yamit Cohen‐Tayar, Shira Rockowitz, Carola Wilczek, Ruth Ashery‐Padan, David Shechter, Deyou Zheng, Aleš Cvekl
Software Mentions: 2
Published: about 8 years ago

10.15252/embr.201744807

<scp>PAWS</scp> 1 controls Wnt signalling through association with casein kinase 1α
Cited by: 24
Author(s): Polyxeni Bozatzi, Kevin S. Dingwell, Kevin Z. L. Wu, Fay Cooper, Timothy D. Cummins, Luke D. Hutchinson, J. Vogt, Nicola T. Wood, Thomas Macartney, Joby Varghese, Robert Gourlay, David G. Campbell, James C. Smith, Gopal P. Sapkota
Software Mentions: 2
Published: over 6 years ago

10.1002/2211-5463.12997

Cystatin C regulates the cytotoxicity of infection‐induced endothelial‐derived β‐amyloid
Cited by: 2
Author(s): Ron Balczon, K. Adam Morrow, Silas J. Leavesley, C.M. Francis, T. Stevens, Ezinne Agwaramgbo, Christopher Williams, R.P. Stevens, Geri Langham, S.B. Voth, Eugene A. Cioffi, Susan E Weintraub, Troy Stevens
Software Mentions: 2
Published: about 4 years ago

10.3389/fpls.2018.01882

Development of a Rapid in planta BioID System as a Probe for Plasma Membrane-Associated Immunity Proteins
Cited by: 37
Author(s): Brendon Conlan, Thomas Stoll, Jeffrey J. Gorman, Isabel M. L. Saur, John P. Rathjen
Software Mentions: 2
Published: almost 6 years ago

10.1093/bioinformatics/btaa288

HiC-Hiker: a probabilistic model to determine contig orientation in chromosome-length scaffolds with Hi-C
Cited by: 11
Author(s): Ryo Nakabayashi, Shinichi Morishita
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-019-5750-x

Waking the sleeping dragon: gene expression profiling reveals adaptive strategies of the hibernating reptile Pogona vitticeps
Cited by: 14
Author(s): Alexander Capraro, Denis O’Meally, Shafagh A. Waters, Hardip R. Patel, Arthur Georges, Paul D. Waters
Software Mentions: 2
Published: over 5 years ago

10.1016/j.bbapap.2013.04.004

A tutorial for software development in quantitative proteomics using PSI standard formats
Cited by: 5
Author(s): Faviel F. Gonzalez-Galarza, Da Qi, Jun Fan, Conrad Bessant, Andrew R. Jones
Software Mentions: 2
Published: almost 11 years ago

10.15252/embj.201798714

Evidence for the nuclear import of histones H3.1 and H4 as monomers
Cited by: 39
Author(s): Michael James Apta‐Smith, Juan R. Hernández-Fernaud, Andrew Bowman
Software Mentions: 2
Published: about 6 years ago

10.1093/database/bav056

Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications
Cited by: 24
Author(s): Tamás Hegedűs, Pururawa Mayank Chaubey, György Várady, Edit Szabó, Hajnalka Sarankó, Lia Hofstetter, Bernd Roschitzki, Bruno Stieger, Balázs Sarkadi
Software Mentions: 2
Published: over 9 years ago

10.1242/dev.185421

Ykt6-dependent endosomal recycling is required for Wnt secretion in the <i>Drosophila</i> wing epithelium
Cited by: 13
Author(s): Karen Linnemannstöns, Leonie Witte, Pradhipa Karuna, Jeanette Clarissa Kittel, Adi Danieli, Denise Madeddu, Lena Nitsch, Mona Honemann‐Capito, Ferdi Grawe, Andreas Wodarz, Julia Christina Gross
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.dib.2020.106064

Tandem mass tagged dataset used to characterize muscle-specific proteome changes in beef during early postmortem period
Cited by: 2
Author(s): Chaoyu Zhai, B. A. Djimsa, Kitty Brown, Jessica E. Prenni, D. R. Woerner, K. E. Belk, Mahesh N. Nair
Software Mentions: 2
Published: about 4 years ago

10.1038/s42003-021-02214-x

Placental secretome characterization identifies candidates for pregnancy complications
Cited by: 16
Author(s): Tina Napso, Xiaohui Zhao, Marta Ibañez-Lligoña, Ionel Sandovici, Richard G. Kay, Amy L. George, Fiona M. Gribble, Frank Reimann, Claire L Meek, Russell S. Hamilton, Amanda N. Sferruzzi‐Perri
Software Mentions: 2
Published: over 3 years ago

10.1016/j.dib.2015.02.013

Supporting data for comparative proteomic analysis of Listeria monocytogenes ATCC 7644 exposed to a sublethal concentration of nisin
Cited by: 0
Author(s): Kendi Nishino Miyamoto, Karina Mariante Monteiro, Karin da Silva Caumo, Karina Rodrigues Lorenzatto, Henrique Bunselmeyer Ferreira, Adriano Brandelli
Software Mentions: 2
Published: over 9 years ago

10.1038/s42003-020-1091-1

Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms
Cited by: 25
Author(s): Yongxin Li, Akihito Omori, Rachel L. Flores, Sheri Satterfield, Christine Nguyen, Tomomi Ota, Toko Tsurugaya, Tetsuro Ikuta, Kazuho Ikeo, Mani Kikuchi, Jason Cheok Kuan Leong, Adrian Reich, Hao Meng, Wenting Wan, Yang Dong, Yaondong Ren, Si Zhang, Tao Zeng, Masahiro Uesaka, Yui Uchida, Xueyan Li, Tomoko Shibata, Takahiro Bino, Kota Ogawa, Shuji Shigenobu, Mariko Kondo, Fayou Wang, Luonan Chen, Gary M. Wessel, Hidetoshi Saiga, R. Andrew Cameron, Brian T. Livingston, Cynthia A. Bradham, Wen Wang, Naoki Irie
Software Mentions: 2
Published: over 4 years ago

10.1186/s12014-019-9228-2

Rapid detection of colistin resistance protein MCR-1 by LC–MS/MS
Cited by: 11
Author(s): Honghui Wang, Yong Chen, Jeffrey R Strich, Steven K. Drake, Jung Ho Youn, Avi Z. Rosenberg, Marjan Guček, Patrick T. McGann, Anthony F. Suffredini, John P. Dekker
Software Mentions: 2
Published: over 5 years ago

10.1186/s12014-017-9172-y

A proteomic approach to understanding the pathogenesis of idiopathic macular hole formation
Cited by: 10
Author(s): Pingbo Zhang, Mingyan Zhu, Yuming Zhao, Jiang Qian, Craig Dufresne, Randi Turner, Richard D. Semba, Sharon D. Solomon
Software Mentions: 2
Published: about 7 years ago

10.1016/j.dib.2014.09.006

Data set for the proteomic inventory and quantitative analysis of chicken uterine fluid during eggshell biomineralization
Cited by: 12
Author(s): Pauline Marie, Valérie Labas, Aurélien Brionne, Grégoire Harichaux, Christelle Hennequet-Antier, Yves Nys, Joël Gautron
Software Mentions: 2
Published: almost 10 years ago

10.3390/cells8020192

In-Depth Proteome Analysis Highlights HepaRG Cells as a Versatile Cell System Surrogate for Primary Human Hepatocytes
Cited by: 35
Author(s): Georg Tascher, Audrey Burban, Sandrine Camus, Marine Plumel, Stéphanie Chanon, Rémy Le Guével, В. П. Шевченко, Alain Van Dorsselaer, Étienne Lefai, Christiane Guguen‐Guillouzo, Fabrice Bertile
Software Mentions: 2
Published: over 5 years ago

10.3390/cells9092070

Dynamic High-Sensitivity Quantitation of Procollagen-I by Endogenous CRISPR-Cas9 NanoLuciferase Tagging
Cited by: 7
Author(s): Ben Calverley, Karl E. Kadler, Adam Pickard
Software Mentions: 2
Published: about 4 years ago

10.3390/cells7120269

Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress
Cited by: 15
Author(s): Meenakshi Agarwal, Ashish Pathak, Rajesh Rathore, Om Prakash, Rakesh Singh, Rajneesh Jaswal, John C. Seaman, Ashvini Chauhan
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.celrep.2021.109230

Integrin intra-heterodimer affinity inversely correlates with integrin activatability
Cited by: 11
Author(s): Guangyu Sun, Emilie Guillon, Scott A. Holley
Software Mentions: 2
Published: over 3 years ago

10.1038/s41419-021-03589-9

Non-canonical role of wild-type SEC23B in the cellular stress response pathway
Cited by: 3
Author(s): Lamis Yehia, Darren Liu, Shuai Fu, Pranav Iyer, Charis Eng
Software Mentions: 2
Published: over 3 years ago

10.1007/s00401-021-02285-4

Age-associated insolubility of parkin in human midbrain is linked to redox balance and sequestration of reactive dopamine metabolites
Cited by: 26
Author(s): Jacqueline M. Tokarew, Daniel N. El-Kodsi, Nathalie A. Lengacher, Travis K. Fehr, Antoinette Nguyen, Bojan Shutinoski, Brian O’Nuallain, Ming Jin, Jasmine Khan, Andy Cheuk-Him Ng, Juan Li, Quan Jiang, Mei Zhang, Liqun Wang, Rajib Sengupta, Kathryn R. Barber, An Tran, Doo Soon Im, Steve Callaghan, David Park, Stéphanie Zandee, Xiajun Dong, Clemens R. Scherzer, Alexandre Prat, Eve C. Tsai, Masashi Takanashi, Nobutaka Hattori, Jennifer A. Chan, Luigi Zecca, Andrew B. West, Arne Holmgren, Lawrence G. Puente, Gary S. Shaw, Gergely Tóth, John Woulfe, Peggy Taylor, Julianna J. Tomlinson, Michael G. Schlossmacher
Software Mentions: 2
Published: over 3 years ago

10.1186/1559-0275-11-23

Deciphering the peptidome of urine from ovarian cancer patients and healthy controls
Cited by: 36
Author(s): Christopher R. Smith, Ihor Batruch, Josep Miquel Bauça, Hari Kosanam, Julia Ridley, Marcus Q. Bernardini, Felix Leung, Eleftherios P. Diamandis, Vathany Kulasingam
Software Mentions: 2
Published: over 10 years ago

10.3389/fpls.2017.01416

Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis
Cited by: 12
Author(s): Zhijian Jiang, Manoj Kumar, Matthew P. Padula, Mathieu Pernice, Tim Kahlke, Mikael Kim, Peter J. Ralph
Software Mentions: 2
Published: over 7 years ago

10.1186/2045-3701-3-37

Proteomic analysis of mismatch repair-mediated alkylating agent-induced DNA damage response
Cited by: 4
Author(s): Xi Chen, Yong Zhao, Guo Min Li, Lin Guo
Software Mentions: 2
Published: about 11 years ago

10.3390/cancers13143618

TRAF6 Phosphorylation Prevents Its Autophagic Degradation and Re-Shapes LPS-Triggered Signaling Networks
Cited by: 3
Author(s): Julia Busch, Rita Moreno, Laureano de la Vega, Vera V. Saul, Susanne Bacher, Felix von Zweydorf, Marius Ueffing, Axel Weber, Christian Johannes Gloeckner, Uwe Linne, Michael Kracht, M. Lienhard Schmitz
Software Mentions: 2
Published: over 3 years ago

10.1186/s12964-018-0257-7

Kv1.3 channel blockade with the Vm24 scorpion toxin attenuates the CD4+ effector memory T cell response to TCR stimulation
Cited by: 19
Author(s): José Ignacio Veytia-Bucheli, Juana María Jiménez-Vargas, Erika Melchy-Pérez, Monserrat Alba Sandoval-Hernández, Lourival D. Possani, Yvonne Rosenstein
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0221669

Cholinergic-like neurons carrying PSEN1 E280A mutation from familial Alzheimer’s disease reveal intraneuronal sAPPβ fragments accumulation, hyperphosphorylation of TAU, oxidative stress, apoptosis and Ca2+ dysregulation: Therapeutic implications
Cited by: 16
Author(s): Viviana Soto-Mercado, Miguel Mendivil-Perez, Carlos Vélez-Pardo, Francisco Lopera, Marlene Jiménez-Del-Río
Software Mentions: 2
Published: over 4 years ago

10.1038/mt.2016.112

Long Non-coding RNA BGas Regulates the Cystic Fibrosis Transmembrane Conductance Regulator
Cited by: 26
Author(s): Sheena Saayman, Amanda Ackley, Jon Burdach, Matthew Clemson, Dieter C. Gruenert, Kiyoshi Tachikawa, Pad Chivukula, Marc S. Weinberg, Kevin V. Morris
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0115213

Microtubule-Dependent Modulation of Adhesion Complex Composition
Cited by: 37
Author(s): Daniel Ng, Jonathan D. Humphries, Adam Byron, Angélique Millon‐Frémillon
Software Mentions: 2
Published: almost 10 years ago